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This page was generated on 2015-10-25 13:31:20 -0400 (Sun, 25 Oct 2015).
| Package 812/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| PSICQUIC 1.8.1 Paul Shannon
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | ||||||
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: PSICQUIC |
| Version: 1.8.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PSICQUIC_1.8.1.tar.gz |
| StartedAt: 2015-10-25 06:34:35 -0400 (Sun, 25 Oct 2015) |
| EndedAt: 2015-10-25 06:36:48 -0400 (Sun, 25 Oct 2015) |
| EllapsedTime: 133.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: PSICQUIC.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PSICQUIC_1.8.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/PSICQUIC.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PSICQUIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PSICQUIC’ version ‘1.8.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PSICQUIC’ can be installed ... [9s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘httr’ ‘plyr’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.loadRegistry: no visible global function definition for ‘DataFrame’
.translate.uniprotkb: no visible binding for global variable ‘id’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘PSICQUIC-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PSICQUIC-class
> ### Title: PSICQUIC
> ### Aliases: class:PSICQUIC PSICQUIC-class PSICQUIC show,PSICQUIC-method
> ### Keywords: methods classes
>
> ### ** Examples
>
> psicquic <- PSICQUIC()
Warning in .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
> # obtain the list of two dozen (or so) currently live
> # PSICQUIC-compliant data providers
> providers(psicquic)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘providers’ for signature ‘"logical"’
Calls: providers -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [10s/30s]
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
test_rawQuery
test_retrieveByDetectionMethod
test_retrieveByInteractionType
test_retrieveByOmimId
test_retrieveByPubmedID
test_retrieveByPubmedIdOnly
test_retrieveBySpeciesId
test_smallMoleculeWithoutSpeciesDesignation
Error in BiocGenerics:::testPackage("PSICQUIC") :
unit tests failed for package PSICQUIC
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/PSICQUIC.Rcheck/00check.log’
for details.
PSICQUIC.Rcheck/tests/runTests.Rout.fail:
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("PSICQUIC")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Attaching package: 'plyr'
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:httr':
content
Loading required package: DBI
checking for biomart access...
does 'http://www.biomart.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.categorize"
[1] "--- test_.translate.ensemblGene"
checking for biomart access...
does 'http://www.biomart.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.translate.ensemblProt"
[1] "--- test_.translate.locuslink"
[1] "--- test_.translate.refseq"
[1] "--- test_.translate.string"
[1] "--- test_.translate.uniprotkb"
[1] "--- test_translateAll"
[1] "--- test_addGeneInfo"
[1] "--- test_addGeneInfoMinimalTable"
checking for biomart access...
does 'http://www.biomart.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_addStandardNames"
[1] "--- test_ctor"
checking for biomart access...
does 'http://www.biomart.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_preserveKnownGeneIdentifiers"
Loading required package: bitops
[1] "--- test_.enumerateSearchPairs"
[1] "--- test_.loadRegistry"
Timing stopped at: 0.004 0 0.288
Error in checkEquals(colnames(tbl), c("url")) :
target is NULL, current is character
In addition: Warning message:
In PSICQUIC:::.loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
[1] "--- test_.restrictBySpecies"
Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.007 0.001 0.292
Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
[1] "--- test_.retrieveData"
Timing stopped at: 0.004 0.001 0.291
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
In addition: Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
[1] "--- test_ctor"
Timing stopped at: 0.003 0 0.289
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
In addition: Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
[1] "--- test_handleEmbeddedSingleQuote"
Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.008 0 0.293
Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
[1] "--- test_initialConditions"
[1] "--- test_interactions"
Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.006 0 0.295
Error in providers %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
[1] "--- test_interactionsFourGenes"
Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.008 0.001 0.296
Error in providers %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
[1] "--- test_interactionsTwoGenes"
Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.006 0.001 0.293
Error in providers %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
[1] "--- test_rawQuery"
Timing stopped at: 0.004 0 0.292
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
In addition: Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.008 0 0.293
Error in providers %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
[1] "--- test_retrieveByInteractionType"
Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.008 0.001 0.295
Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
[1] "--- test_retrieveByOmimId"
Timing stopped at: 0.004 0.001 0.29
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'interactions' for signature '"logical"'
In addition: Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
[1] "--- test_retrieveByPubmedID"
Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.007 0 0.294
Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
[1] "--- test_retrieveByPubmedIdOnly"
Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.008 0 0.296
Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
[1] "--- test_retrieveBySpeciesId"
Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.009 0.001 0.296
Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
[1] "--- test_smallMoleculeWithoutSpeciesDesignation"
Warning message:
In .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.009 0.001 0.299
Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
RUNIT TEST PROTOCOL -- Sun Oct 25 06:36:39 2015
***********************************************
Number of test functions: 31
Number of errors: 15
Number of failures: 1
1 Test Suite :
PSICQUIC RUnit Tests - 31 test functions, 15 errors, 1 failure
FAILURE in test_.loadRegistry: Error in checkEquals(colnames(tbl), c("url")) :
target is NULL, current is character
ERROR in test_.restrictBySpecies: Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
ERROR in test_.retrieveData: Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
ERROR in test_ctor: Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
ERROR in test_handleEmbeddedSingleQuotes: Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
ERROR in test_interactions: Error in providers %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
ERROR in test_interactionsFourGenes: Error in providers %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
ERROR in test_interactionsTwoGenes: Error in providers %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
ERROR in test_rawQuery: Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
ERROR in test_retrieveByDetectionMethod: Error in providers %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
ERROR in test_retrieveByInteractionType: Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
ERROR in test_retrieveByOmimId: Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'interactions' for signature '"logical"'
ERROR in test_retrieveByPubmedID: Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
ERROR in test_retrieveByPubmedIdOnly: Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
ERROR in test_retrieveBySpeciesId: Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
ERROR in test_smallMoleculeWithoutSpeciesDesignation: Error in provider %in% providers(psicquic) :
error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>
Test files with failing tests
test_PSICQUIC.R
test_.loadRegistry
test_.restrictBySpecies
test_.retrieveData
test_ctor
test_handleEmbeddedSingleQuotes
test_interactions
test_interactionsFourGenes
test_interactionsTwoGenes
test_rawQuery
test_retrieveByDetectionMethod
test_retrieveByInteractionType
test_retrieveByOmimId
test_retrieveByPubmedID
test_retrieveByPubmedIdOnly
test_retrieveBySpeciesId
test_smallMoleculeWithoutSpeciesDesignation
Error in BiocGenerics:::testPackage("PSICQUIC") :
unit tests failed for package PSICQUIC
Execution halted
PSICQUIC.Rcheck/00install.out:
* installing *source* package ‘PSICQUIC’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (PSICQUIC)
PSICQUIC.Rcheck/PSICQUIC-Ex.timings:
| name | user | system | elapsed | |
| IDMapper-class | 0.226 | 0.010 | 3.201 | |